I would go even further and point out how Harry's arrogance is good for the story. Here's my approach to this critique:
"You're absolutely right that Harry!HPMOR is arrogant and condescending. It is a clear character flaw, and repeatedly gets in the way of his success. As part of a work of fiction, this is exactly how things should be. All people have flaws, and a story with a character with not flaws wouldn't be interesting to read!
Harry suffers significantly due to this trait, which is precisely what a good author does with their characters.
Later on there is an entire section dedicated to Harry learning "how to lose," and growing to not be quite as blind in this way. If his character didn't have anywhere to develop, it wouldn't be a very good story!"
While this is true, there can be a distinction between a character with flaws and a character who is extremely irritating to read about. And this is one of those judgement calls where The Audience is Always Right; it seems very reasonable to stop reading a story if the protagonist noticeably irritates you.
In general, commentary to the effect of "you should like this thing" is not very useful, especially if you are trying to figure out why someone reacted negatively.
(These discussions in which one group has an overwhelmingly strong "squick&...
I was reading reviews of HPMOR on Goodreads and I noticed that the people who didn't like the book were essentially "put off by the rationality". They thought Harry was arrogant and condescending.
Then I was thinking, a lot of people are "put off by rationality" for similar reasons. What a shame. There's a lot of value in spreading rationality, and this seems to be a big obstacle in doing so.
Any thoughts on how to make people less "put off by rationality"? I think the core issues are: